It's not a fallacy, and no one is saying "we see Y, therefore X is true." We are saying, if X is true we should expect to see Y. And we do that over and over and over again, for different predictions. And we evaluate predictions for alternative hypotheses as well. For evolution this has been going on for 150 years and everything we have learned about biology in that time has affirmed evolutionary theory. That gives us a strong indication that it is correct. Yes, it could also be a designer, but in the case of a designer you could say it was designed that way no matter what you see, which is why I say it is not falsifiable and therefore not science.
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Ok, I stand corrected on the fallacy thing, provided you are not actually standing on these predictions as proofs.
But to say that everything we have learned about biology for the last 150 years affirms evolutionary theory can only be true if you are wearing a particular color of glasses. There are many biological processes and constructs which evolutionary theory cannot explain except with the most optimistic hypotheses. I have never heard of a good refutation of irreducible complexity, for example. There are myriad elements in biological systems which would have no use and no contribution to the survival of the fittest by themselves, and many systems which can only work if all the elements are first in place.